A DNA

Mirkin C A ef a/1996 A DNA-based method for rationally assembling nanopartioles into maorosoopio materials Nature 382 607... 

Eisenstein, M., Shakked, Z.i Hydration patterns and intermolecnlar interactions in A-DNA crystal structures. Implications for DNA recognition. J. Mol. Biol. 248 (1995) 662-678... 

Gap A break in a DNA or protein sequence which enables two or more sequence to be aligned... 

CR Polymerase Chain Reaction. Widely used method for amplifying a DNA base sequence... 

A DNA double helix as pic tured on a 1964 postage stamp issued by Israel... 

The structure proposed by Watson and Crick was modeled to fit crystallographic data obtained on a sample of the most common form of DNA called B DNA Other forms include A DNA which is similar to but more compact than B DNA and Z DNA which IS a left handed double helix... 

By analogy to the levels of structure of proteins the primary structure of DNA IS the sequence of bases along the polynucleotide chain and the A DNA B DNA and Z DNA helices are varieties of secondary structures... 

FIGURE 28 5 (a) Tube and (b) space filling models of a DNA double helix The carbohydrate-phosphate backbone is on the out side and can be roughly traced in (b) by the red oxygen atoms The blue atoms belong to the purine and pyrimidine bases and he on the inside The base pairing is more clearly seen in (a)... 

FIGURE 28 10 During transcription a molecule of mRNA is assembled from a DNA template Transcription begins at a promoter sequence and proceeds in the 5 3 direction of the mRNA until a termination sequence of the DNA is reached Only a region of about 10 base pairs is unwound at any time... 

The viruses responsible for AIDS are human immunodeficiency virus 1 and 2 (HIV 1 and HIV 2) Both are retroviruses, meaning that their genetic material is RNA rather than DNA HI Vs require a host cell to reproduce and the hosts m humans are the T4 lymphocytes which are the cells primarily responsible for inducing the immune system to respond when provoked The HIV penetrates the cell wall of a T4 lymphocyte and deposits both its RNA and an enzyme called reverse transcriptase inside There the reverse transcriptase catalyzes the formation of a DNA strand that is complementary to the viral RNA The transcribed DNA then serves as the template from which the host lymphocyte produces copies of the virus which then leave the host to infect other T4 cells In the course of HIV reproduction the ability of the T4 lymphocyte to reproduce Itself IS compromised As the number of T4 cells decrease so does the body s ability to combat infections... 

The contents of each tube are then subjected to electrophoresis m separate lanes on the same sheet of polyacrylamide gel and the DNAs located by autoradiography A typical electrophoresis gel of a DNA fragment containing 50 nucleotides will exhibit a pattern of 50 bands distributed among the four lanes with no overlaps Each band cor responds to a polynucleotide that is one nucleotide longer than the one that precedes it (which may be m a different lane) One then simply reads the nucleotide sequence according to the lane m which each succeeding band appears... 

The mam use of PCR is to amplify or make hundreds of thousands—even mil lions—of copies of a portion of the polynucleotide sequence m a sample of DNA Sup pose for example we wish to copy a 500 base pair region of a DNA that contains a total of 1 million base pairs We would begin as described m Section 28 14 by cleaving the DNA into smaller fragments using restriction enzymes then use PCR to make copies of the desired fragment... 

Each primer is a synthetic oligonucleotide of about 20 bases prepared so that then-sequences are complementary to the (previously determined) sequences that flank the tar get regions on opposite strands Thus one primer is annealed to one strand the other to the other strand The 3 hydroxyl end of each primer points toward the target region The stage is now set for DNA synthesis to proceed from the 3 end of each primer [Figure 28 14(c )] The solution contains a DNA polymerase and Mg " m addition to the... 

Section 28 11 Three RNAs are involved m gene expression In the transcription phase a strand of messenger RNA (mRNA) is synthesized from a DNA tern plate The four bases A G C and U taken three at a time generate 64 possible combinations called codons These 64 codons comprise the genetic code and code for the 20 ammo acids found m proteins plus start and stop signals The mRNA sequence is translated into a prescribed protein sequence at the ribosomes There small polynucleotides called... 

Nucleosome (Section 28 9) A DNA-protem complex by which DNA IS stored in cells... 

Transcription (Section 28 11) Construction of a strand of mRNA complementary to a DNA template Transfer RNA (tRNA) (Section 28 11) A polynucleotide of n hose that is bound at one end to a unique amino acid This ammo acid is incorporated into a growing peptide chain Transition state (Section 3 1) The point of maximum energy in an elementary step of a reaction mechanism Translation (Section 28 12) The reading of mRNA by van ous tRNAs each one of which is unique for a particular ammo acid... 

A chain of nucleotides containing only deoxyribose as the sugar is a DNA. Similarly, RNA possesses chains nucleotides having only ribose as the sugar and is therefore a ribonucleic acid. 

Fig. 6. DNA sequence analysis, (a) Simplified methodology for dideoxy sequencing. A primer, 5 -TCTA, hybridized to the template, is used to initiate synthesis by DNA polymerase, (b) Stmcture of 2, 3 -dideoxy CTP. When no 3 -OH functionaUty is available to support addition of another nucleotide to the growing chain, synthesis terminates once this residue is incorporated into the synthetic reaction, (c) Representation of a DNA sequencing gel and the sequence, read from bottom to the top of the gel, gives sequence information in the conventional 5 to 3 direction.

PGR amplification of a DNA sequence is faciHtated by the use of a heat-stable DNA polymerase, Taq polymerase (TM), derived from the thermostable bacterium Thermus aquaticus. The thermostable polymerase allows the repeated steps of strand separation, primer annealing, and DNA synthesis to be carried out ia a single reactioa mixture where the temperature is cycled automatically. Each cycle coasists of a high temperature step to deaature the template strands, a lower temperature annealing of the primer and template, and a higher temperature synthesis step. AH components of the reaction are present ia the same tube. 

Many human diseases are caused when certain proteins are either over- or underexpressed. Eor example, breast cancer can be induced by overexpressing certain cellular oncogenes within mammary tissue. To study the disease, researchers produce a line of transgenic mice that synthesize an abnormal amount of the same protein. This leads to symptoms of the disease in mice that are similar to what is found in humans. A protein can be overexpressed by inserting a DNA constmct with a strong promotor. Conversely, underexpression of a protein can be achieved by inserting a DNA constmct that makes antisense RNA. This latter blocks protein synthesis because the antisense RNA binds and inactivates the sense mRNA that codes for the protein. Once a line of mice is developed, treatments are studied in mice before these therapies are appHed to humans. 

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